DOCK GA Parameters
From Rizzo_Lab
| Parameter | Description | Default Value |
|---|---|---|
| ga_molecule_file | Initial molecule ensemble in mol2 format | - |
| ga_fraglib_scaffold_file | Fragment library mol2 file containing scaffolds | - |
| ga_fraglib_linker_file | Fragment library mol2 file containing linkers | - |
| ga_fraglib_sidechain_file | Fragment library mol2 file containing side chains | - |
| ga_use_torenv_table | Is the user going to use a torsion environment table (.dat) | yes |
| ga_torenv_table | Path to the torsion environment table (.dat) | - |
| ga_use_dn_roulette | Is the user going to use a roulette acceptance for torsions | no |
| ga_max_generations | Max number of generations to be executed | 100 |
| ga_xover_sampling_method_rand | Selects the random or exhaustive crossover sampling methods (yes for random) | yes |
| ga_xover_max | Max number of offspring generated from crossover events | 150 |
| ga_bond_tolerance | User-specified cutoff for allowable atom sq dist | 0.5 |
| ga_angle_cutoff | User-specified cutoff for bond angles | 0.14 |
| ga_check_overlap | Output parent pairs involved in crossover in unique_xover.mol2 file | no |
| ga_mutations | Turn on mutations | yes |
| ga_mutate_addition | Turn on mutation type addition | yes |
| ga_mutate_deletion | Turn on mutation type deletion | yes |
| ga_mutate_substitution | Turn on mutation type substitution | yes |
| ga_mutate_replacement | Turn on mutation type replacement (also known as scaffold hopping) | yes |
| ga_mutate_parents | Mutate the parents | no |
| ga_pmut_rate | Parent mutation rate - only used when random parent mutation is turned on | 0.3 |
| ga_omut_rate | Offspring mutation rate for random mutation sampling | 0.7 |
| ga_max_mut_cycles | Max mutation attemps - for random mutation sampling | 5 |
| ga_mut_sampling_method | Type of sampling (rand, graph) | rand |
| ga_num_random_picks | Number of random picks for random sampling | 10 |
| ga_max_root_size | Max root size in NOVA | 5 |
| ga_graph_max_picks | The number of fragment picks per round of mutation when grpah method is turned on | 10 |
| ga_graph_breadth | The number of fragments that are similar (using Tanimoto) to a successful fragment when graph method is turned on | 3 |
| ga_graph_depth | Parameter that controls the overall number of fragment attempted via the following formula: Total_attempts=(breadth)^(depth) | 2 |
| ga_graph_temperature | The initial annealing temperature when the graph method is turned on | 100 |
| ga_energy_cutoff | The upper bounds for energy pruning | 100 |
| ga_heur_unmatched_num | The number of unmatched atoms for H. RMSD pruning | 5 |
| ga_heur_matched_rmsd | The RMSD of matched atoms for H. RMSD pruning | 2.0 |
| ga_constraint_mol_wt | The upper bound for mol wt | 500 |
| ga_constraint_rot_bon | The upper bound for # rot bonds | 10 |
| ga_constraint_H_accept | The upper bound for # of hydrogen acceptors | 10 |
| ga_constraint_H_donor | The upper bound for # of hydrogen donors | 5 |
| ga_constraint_formal_charge | The upper and lower bound for formal charge | 4 |
| ga_ensemble_size | The number of survivors to carry to next generation | 200 |
| ga_selection_method | Type of selection (elitism, tournament, roulette) | elitism |
| ga_elitism_combined | Combine the parent and offspring populations for the elitism selection method? | no |
| ga_elitism_option | Type of selection: max, percent, or number when elitism is the selection method | max |
| ga_elitism_number | The number of top scored parents to pass to the next generation when elitism number is the selection method | 20 |
| ga_elitism_percent | The top percent of the ensemble(s) to be carried tot he next generation when elitism percent is the selection method | 0.2 |
| ga_tournament_p_vs_c | Select the top scored molecules between parents and offspring separately when tournament selection method is used | yes |
| ga_roulette_separate | Select the top scored molecule between parents and offspring separately when roulette selection method is used | yes |
| ga_niching | Selection niching method | no |
| ga_niching_method | Type of selection (sharing crowding) when niching is turned on | sharing |
| ga_selection_extinction | Turn on mass extinction? | no |
| ga_extinction_frequency | Number of generations to turn on when mass extinction is used | 200 |
| ga_extinction_duration | Number of generations to remain on when mass extinction is used | 50 |
| ga_extinction_keep | Number of generations to remain on when mass extinction is used | 20 |
| ga_extinction_switch_selection | Change selection type when mass extinction is used | no |
| ga_secondary_selection_method | Secondary selection when ga_extinction_switch_selection = yes (Options: elitism, roulette, tournament) | roulette |
| ga_max_num_gen_with_no_crossover | The max generation of allowable growth without a crossover event | 5 |
| ga_output_prefix | User-defined output name prefix | output |
